Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects.

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PubMed ID: 30745895

Imagen Publicación

Camelo-Castillo A, Henares D, Brotons P, Galiana A, Rodríguez JC, Mira A, Muñoz-Almagro C

Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00011

COMMENT: Nasopharyngeal microbiota could be an important factor to understand susceptibility to pulmonary infections like Invasive Pneumococcal Disease (IPD) caused by Streptococcus pneumoniae. This work describes the use of a long-amplicon (780 pb) sequencing approach of the 16S rRNA (V1-V4) for improvement of taxonomic identification, in a case-control study of the nasopharyngeal microbiota of children with IPD and healthy children.


To characterize the nasopharyngeal microbiota profiles in two groups of children: (i) children with invasive pneumococcal disease (IPD), considered as a case group whose nasopharyngeal microbiota was suffering an important disturbance; and (ii) a matched control group of healthy children representative of a healthy nasopharyngeal niche. A series of epidemiological, microbiological, and clinical variables related with major risk of developing IPD were considered to compare microbiota profiles in the two groups. For robust characterization of bacterial composition, a long-fragment 16S sequencing approach was used...

Main results

Our data show that bacterial richness and diversity were significantly higher in IPD patients. In such cases, a clear dysbiosis was observed with a high frequency of Veillonella and other oral microorganisms which appeared to be relatively absent in controls.

The taxonomic assignment of the 16S rRNA reads revealed that the most common phyla in IPD patients were Firmicutes (50.9% of the total number of reads), Proteobacteria (41.4%), Bacteroidetes (5.0%), Actinobacteria (2.2%), and a lower proportion of Fusobacteria. Within the control group, the most common phyla were Proteobacteria (66.0% of the total number of reads), Firmicutes (33.6%), Bacteroidetes (0.2%), and Actinobacteria (0.2%).

In the cases group the most prevalent bacteria were Streptococcus, Haemophilus, Moraxella, Dolosigranulum, Veillonella, and Staphylococcus

Our data identified three bacterial clusters or nasopharyngeal-types, nasopharyngeal-type A was dominated by Dolosigranulum, nasopharyngeal-type C by Haemophilus, and nasopharyngeal-type B by Streptococcus.

the only statistically significant explanatory factor for these three microbiota profiles was the classification of patients into case or control groups. Streptococcus-dominated community (Microbiota B) was clearly associated to IPD patients.

we found a considerably higher proportion of Microbiota A healthy controls that were breastfed and a trend for statistical significance in the relation between exclusive breastfeeding up to 6 months of age and case-control classification (p = 0.06)

In order to understand the features influencing nasopharyngeal-types, all available epidemiological, microbiological, immunological and clinical variables were compared by bivariate analysis with the three microbiota types. No significant differences were found in any of the variables considered that could explain the grouping in the three different microbiotas


We found a higher bacterial diversity and richness in children with IPD which could suggest an impaired immune response.

We found suggestive microbiota profiles associated to IPD (Streptococcus-dominated microbiota profile) or asymptomatic colonization (Dolosigranulum-dominated microbiota profile) that could be used, respectively, as disease biomarkers or to identify health-associated inhabitants of the respiratory tract.

The characterization of beneficial bacteria could be useful to prevent pneumococcal infections by integrating those microorganisms in a probiotic formula. The present study suggests not only respiratory tract samples, but also breast milk, as a potential source of those beneficial bacteria.


Diana López-Farfán